# An Evolutionary Framework For Identifying Determinants Of Colonization In Human Microbiomes

> **NIH NIH DP2** · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · 2020 · $2,259,000

## Abstract

AN EVOLUTIONARY FRAMEWORK FOR IDENTIFYING
DETERMINANTS OF COLONIZATION IN HUMAN MICROBIOMES
Rational probiotic therapies for our gut, skin, and other microbiomes have the potential to treat a wide
range of diseases and promote wellness. However, we still lack basic knowledge about how bacterial
strains colonize in the microbiome, such that it is difficult to predict if a particular bacterial strain will
colonize an individual.
Engineering human microbiomes will require human-specific knowledge that is difficult to infer from in
vitro and animal models. My central vision is to use modeling and reconstruction of within-person
evolution to infer recent bacterial natural history in human microbiomes with high precision.
We will develop computational tools for high-through analysis of single-organism genomes and strain-
level inference in metagenomic data. Using a combination of these tools and in-human studies, we will
understand the colonization dynamics and on-person spreading of many commensal strains, determine
the drivers and molecular strategies of within-person bacterial adaptation, and determine the degree to
which within-person selection is person-specific. We will also investigate the connection between
within-person evolution and community stability.
This novel population-genetics paradigm will bound expectations for interpreting metagenomic data and
offer clues on how to precisely manipulate human microbiomes, with the potential to lay the groundwork
for the selection of probiotic strains with the highest chance of engraftment.

## Key facts

- **NIH application ID:** 10001088
- **Project number:** 1DP2GM140922-01
- **Recipient organization:** MASSACHUSETTS INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** Tami D Lieberman
- **Activity code:** DP2 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $2,259,000
- **Award type:** 1
- **Project period:** 2020-09-30 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10001088

## Citation

> US National Institutes of Health, RePORTER application 10001088, An Evolutionary Framework For Identifying Determinants Of Colonization In Human Microbiomes (1DP2GM140922-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10001088. Licensed CC0.

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